{"id":"https://openalex.org/W4407189605","doi":"https://doi.org/10.1038/s42256-024-00978-5","title":"Discovering fully semantic representations via centroid- and orientation-aware feature learning","display_name":"Discovering fully semantic representations via centroid- and orientation-aware feature learning","publication_year":2025,"publication_date":"2025-02-06","ids":{"openalex":"https://openalex.org/W4407189605","doi":"https://doi.org/10.1038/s42256-024-00978-5","pmid":"https://pubmed.ncbi.nlm.nih.gov/40008294"},"language":"en","primary_location":{"id":"doi:10.1038/s42256-024-00978-5","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-024-00978-5","pdf_url":"https://www.nature.com/articles/s42256-024-00978-5.pdf","source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://www.nature.com/articles/s42256-024-00978-5.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5041497735","display_name":"Jaehoon Cha","orcid":"https://orcid.org/0000-0002-2498-4214"},"institutions":[{"id":"https://openalex.org/I162524378","display_name":"Science and Technology Facilities Council","ror":"https://ror.org/057g20z61","country_code":"GB","type":"government","lineage":["https://openalex.org/I162524378","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Jaehoon Cha","raw_affiliation_strings":["Scientific Computing Department, Science and Technology Facilities Council, Harwell, Didcot, UK"],"affiliations":[{"raw_affiliation_string":"Scientific Computing Department, Science and Technology Facilities Council, Harwell, Didcot, UK","institution_ids":["https://openalex.org/I162524378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009759789","display_name":"Jinhae Park","orcid":"https://orcid.org/0000-0003-0159-6187"},"institutions":[{"id":"https://openalex.org/I196345858","display_name":"Chungnam National University","ror":"https://ror.org/0227as991","country_code":"KR","type":"education","lineage":["https://openalex.org/I196345858"]}],"countries":["KR"],"is_corresponding":false,"raw_author_name":"Jinhae Park","raw_affiliation_strings":["Department of Mathematics, Chungnam National University, Daejeon, South Korea"],"affiliations":[{"raw_affiliation_string":"Department of Mathematics, Chungnam National University, Daejeon, South Korea","institution_ids":["https://openalex.org/I196345858"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5021631342","display_name":"Samuel Pinilla","orcid":"https://orcid.org/0000-0002-6653-2363"},"institutions":[{"id":"https://openalex.org/I162524378","display_name":"Science and Technology Facilities Council","ror":"https://ror.org/057g20z61","country_code":"GB","type":"government","lineage":["https://openalex.org/I162524378","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Samuel Pinilla","raw_affiliation_strings":["Scientific Computing Department, Science and Technology Facilities Council, Harwell, Didcot, UK"],"affiliations":[{"raw_affiliation_string":"Scientific Computing Department, Science and Technology Facilities Council, Harwell, Didcot, UK","institution_ids":["https://openalex.org/I162524378"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5018919307","display_name":"Kyle L. Morris","orcid":"https://orcid.org/0000-0002-1717-8134"},"institutions":[{"id":"https://openalex.org/I1303153112","display_name":"European Bioinformatics Institute","ror":"https://ror.org/02catss52","country_code":"GB","type":"facility","lineage":["https://openalex.org/I1303153112","https://openalex.org/I4210138560"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Kyle L. Morris","raw_affiliation_strings":["Electron Microscopy Data Bank, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK"],"affiliations":[{"raw_affiliation_string":"Electron Microscopy Data Bank, European Molecular Biology Laboratory, European Bioinformatics Institute, Hinxton, UK","institution_ids":["https://openalex.org/I1303153112"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056903613","display_name":"Christopher S. Allen","orcid":"https://orcid.org/0000-0002-6353-6000"},"institutions":[{"id":"https://openalex.org/I2802711169","display_name":"Diamond Light Source","ror":"https://ror.org/05etxs293","country_code":"GB","type":"facility","lineage":["https://openalex.org/I2802711169"]},{"id":"https://openalex.org/I40120149","display_name":"University of Oxford","ror":"https://ror.org/052gg0110","country_code":"GB","type":"education","lineage":["https://openalex.org/I40120149"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Christopher S. Allen","raw_affiliation_strings":["Department of Materials, University of Oxford, Oxford, UK","Electron Physical Science Imaging Centre, Diamond Light Source, Didcot, UK"],"affiliations":[{"raw_affiliation_string":"Department of Materials, University of Oxford, Oxford, UK","institution_ids":["https://openalex.org/I40120149"]},{"raw_affiliation_string":"Electron Physical Science Imaging Centre, Diamond Light Source, Didcot, UK","institution_ids":["https://openalex.org/I2802711169"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5009597717","display_name":"M. I. Wilkinson","orcid":"https://orcid.org/0000-0002-2753-7890"},"institutions":[{"id":"https://openalex.org/I153648349","display_name":"University of Leicester","ror":"https://ror.org/04h699437","country_code":"GB","type":"education","lineage":["https://openalex.org/I153648349"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Mark I. Wilkinson","raw_affiliation_strings":["Department of Physics and Astronomy, University of Leicester, Leicester, UK"],"affiliations":[{"raw_affiliation_string":"Department of Physics and Astronomy, University of Leicester, Leicester, UK","institution_ids":["https://openalex.org/I153648349"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008605990","display_name":"Jeyan Thiyagalingam","orcid":"https://orcid.org/0000-0002-2167-1343"},"institutions":[{"id":"https://openalex.org/I162524378","display_name":"Science and Technology Facilities Council","ror":"https://ror.org/057g20z61","country_code":"GB","type":"government","lineage":["https://openalex.org/I162524378","https://openalex.org/I4210087105"]}],"countries":["GB"],"is_corresponding":false,"raw_author_name":"Jeyan Thiyagalingam","raw_affiliation_strings":["Scientific Computing Department, Science and Technology Facilities Council, Harwell, Didcot, UK"],"affiliations":[{"raw_affiliation_string":"Scientific Computing Department, Science and Technology Facilities Council, Harwell, Didcot, UK","institution_ids":["https://openalex.org/I162524378"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5041497735"],"corresponding_institution_ids":["https://openalex.org/I162524378"],"apc_list":{"value":9750,"currency":"EUR","value_usd":11690},"apc_paid":{"value":9750,"currency":"EUR","value_usd":11690},"fwci":3.7259,"has_fulltext":true,"cited_by_count":3,"citation_normalized_percentile":{"value":0.91965557,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":91,"max":99},"biblio":{"volume":"7","issue":"2","first_page":"307","last_page":"314"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T14339","display_name":"Image Processing and 3D Reconstruction","score":0.9883000254631042,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T14339","display_name":"Image Processing and 3D Reconstruction","score":0.9883000254631042,"subfield":{"id":"https://openalex.org/subfields/1707","display_name":"Computer Vision and Pattern Recognition"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T12859","display_name":"Cell Image Analysis Techniques","score":0.9842000007629395,"subfield":{"id":"https://openalex.org/subfields/1304","display_name":"Biophysics"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.9796000123023987,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/centroid","display_name":"Centroid","score":0.8134108781814575},{"id":"https://openalex.org/keywords/autoencoder","display_name":"Autoencoder","score":0.7178791165351868},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.7111486792564392},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6748152375221252},{"id":"https://openalex.org/keywords/orientation","display_name":"Orientation (vector space)","score":0.5978518724441528},{"id":"https://openalex.org/keywords/invariant","display_name":"Invariant (physics)","score":0.5810765027999878},{"id":"https://openalex.org/keywords/pattern-recognition","display_name":"Pattern recognition (psychology)","score":0.5747875571250916},{"id":"https://openalex.org/keywords/encoder","display_name":"Encoder","score":0.5538502931594849},{"id":"https://openalex.org/keywords/computer-vision","display_name":"Computer vision","score":0.466513991355896},{"id":"https://openalex.org/keywords/rotation","display_name":"Rotation (mathematics)","score":0.4506972134113312},{"id":"https://openalex.org/keywords/translation","display_name":"Translation (biology)","score":0.41568851470947266},{"id":"https://openalex.org/keywords/deep-learning","display_name":"Deep learning","score":0.33239802718162537},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.15741431713104248},{"id":"https://openalex.org/keywords/geometry","display_name":"Geometry","score":0.08304023742675781}],"concepts":[{"id":"https://openalex.org/C146599234","wikidata":"https://www.wikidata.org/wiki/Q511093","display_name":"Centroid","level":2,"score":0.8134108781814575},{"id":"https://openalex.org/C101738243","wikidata":"https://www.wikidata.org/wiki/Q786435","display_name":"Autoencoder","level":3,"score":0.7178791165351868},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.7111486792564392},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6748152375221252},{"id":"https://openalex.org/C16345878","wikidata":"https://www.wikidata.org/wiki/Q107472979","display_name":"Orientation (vector space)","level":2,"score":0.5978518724441528},{"id":"https://openalex.org/C190470478","wikidata":"https://www.wikidata.org/wiki/Q2370229","display_name":"Invariant (physics)","level":2,"score":0.5810765027999878},{"id":"https://openalex.org/C153180895","wikidata":"https://www.wikidata.org/wiki/Q7148389","display_name":"Pattern recognition (psychology)","level":2,"score":0.5747875571250916},{"id":"https://openalex.org/C118505674","wikidata":"https://www.wikidata.org/wiki/Q42586063","display_name":"Encoder","level":2,"score":0.5538502931594849},{"id":"https://openalex.org/C31972630","wikidata":"https://www.wikidata.org/wiki/Q844240","display_name":"Computer vision","level":1,"score":0.466513991355896},{"id":"https://openalex.org/C74050887","wikidata":"https://www.wikidata.org/wiki/Q848368","display_name":"Rotation (mathematics)","level":2,"score":0.4506972134113312},{"id":"https://openalex.org/C149364088","wikidata":"https://www.wikidata.org/wiki/Q185917","display_name":"Translation (biology)","level":4,"score":0.41568851470947266},{"id":"https://openalex.org/C108583219","wikidata":"https://www.wikidata.org/wiki/Q197536","display_name":"Deep learning","level":2,"score":0.33239802718162537},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.15741431713104248},{"id":"https://openalex.org/C2524010","wikidata":"https://www.wikidata.org/wiki/Q8087","display_name":"Geometry","level":1,"score":0.08304023742675781},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0},{"id":"https://openalex.org/C55493867","wikidata":"https://www.wikidata.org/wiki/Q7094","display_name":"Biochemistry","level":1,"score":0.0},{"id":"https://openalex.org/C37914503","wikidata":"https://www.wikidata.org/wiki/Q156495","display_name":"Mathematical physics","level":1,"score":0.0},{"id":"https://openalex.org/C105580179","wikidata":"https://www.wikidata.org/wiki/Q188928","display_name":"Messenger RNA","level":3,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1038/s42256-024-00978-5","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-024-00978-5","pdf_url":"https://www.nature.com/articles/s42256-024-00978-5.pdf","source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},{"id":"pmid:40008294","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/40008294","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature machine intelligence","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11847704","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11847704","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11847704/pdf/42256_2024_Article_978.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nat Mach Intell","raw_type":"Text"},{"id":"pmh:oai:figshare.com:article/28381646","is_oa":true,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4377196282","display_name":"Figshare","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210132348","host_organization_name":"Figshare (United Kingdom)","host_organization_lineage":["https://openalex.org/I4210132348"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal contribution"},{"id":"pmh:oai:purl.org/net/epubs:work/60991659","is_oa":true,"landing_page_url":"https://epubs.stfc.ac.uk/work/60991659","pdf_url":null,"source":{"id":"https://openalex.org/S4306400334","display_name":"Science and Technology Facilities Council","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Journal Article"}],"best_oa_location":{"id":"doi:10.1038/s42256-024-00978-5","is_oa":true,"landing_page_url":"https://doi.org/10.1038/s42256-024-00978-5","pdf_url":"https://www.nature.com/articles/s42256-024-00978-5.pdf","source":{"id":"https://openalex.org/S2912241403","display_name":"Nature Machine Intelligence","issn_l":"2522-5839","issn":["2522-5839"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310319908","host_organization_name":"Nature Portfolio","host_organization_lineage":["https://openalex.org/P4310319908","https://openalex.org/P4310319965"],"host_organization_lineage_names":["Nature Portfolio","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nature Machine Intelligence","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4099999964237213,"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production"}],"awards":[{"id":"https://openalex.org/G6861856814","display_name":"Blueprinting AI for Science at Exascale - Phase II (BASE-II)","funder_award_id":"EP/X019918/1","funder_id":"https://openalex.org/F4320334627","funder_display_name":"Engineering and Physical Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320321204","display_name":"Chungnam National University","ror":"https://ror.org/0227as991"},{"id":"https://openalex.org/F4320334627","display_name":"Engineering and Physical Sciences Research Council","ror":"https://ror.org/0439y7842"},{"id":"https://openalex.org/F4320334632","display_name":"Science and Technology Facilities Council","ror":"https://ror.org/057g20z61"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4407189605.pdf","grobid_xml":"https://content.openalex.org/works/W4407189605.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W569478347","https://openalex.org/W2003260632","https://openalex.org/W2044738244","https://openalex.org/W2112193291","https://openalex.org/W2159498975","https://openalex.org/W2742903995","https://openalex.org/W2902476877","https://openalex.org/W2946591934","https://openalex.org/W2954996726","https://openalex.org/W2963038539","https://openalex.org/W3009153763","https://openalex.org/W3112497262","https://openalex.org/W3162692571","https://openalex.org/W3203256536","https://openalex.org/W4310035804","https://openalex.org/W6752145142","https://openalex.org/W6964141309"],"related_works":["https://openalex.org/W3013693939","https://openalex.org/W2566616303","https://openalex.org/W2159052453","https://openalex.org/W3131327266","https://openalex.org/W2734887215","https://openalex.org/W2803255133","https://openalex.org/W4297051394","https://openalex.org/W2752972570","https://openalex.org/W4386815338","https://openalex.org/W2145836866"],"abstract_inverted_index":{"Learning":[0],"meaningful":[1,36],"representations":[2],"of":[3,38,47,70,72,134],"images":[4,92,107,137],"in":[5,13,40],"scientific":[6,88],"domains":[7],"that":[8,34,113],"are":[9],"robust":[10],"to":[11,62,66],"variations":[12],"centroids":[14],"and":[15,25,50,55,68,77,105,118,122,129],"orientations":[16,69,117],"remains":[17],"an":[18,30,56],"important":[19],"challenge.":[20],"Here":[21],"we":[22],"introduce":[23],"centroid-":[24],"orientation-aware":[26],"disentangling":[27],"autoencoder":[28],"(CODAE),":[29],"encoder-decoder-based":[31],"neural":[32],"network":[33],"learns":[35,115],"content":[37],"objects":[39,71],"a":[41,45,48],"latent":[42],"space.":[43],"Specifically,":[44],"combination":[46],"translation-":[49],"rotation-equivariant":[51],"encoder,":[52],"Euler":[53],"encoding":[54],"image":[57],"moment":[58],"loss":[59],"enables":[60],"CODAE":[61,114],"extract":[63],"features":[64,121],"invariant":[65,120],"positions":[67],"interest":[73],"from":[74,93,102,108],"randomly":[75],"translated":[76],"rotated":[78],"images.":[79],"We":[80],"evaluate":[81],"this":[82],"approach":[83],"on":[84],"several":[85],"publicly":[86],"available":[87],"datasets,":[89],"including":[90],"protein":[91],"life":[94],"sciences,":[95],"four-dimensional":[96],"scanning":[97],"transmission":[98],"electron":[99],"microscopy":[100],"data":[101],"material":[103],"science":[104],"galaxy":[106],"astronomy.":[109],"The":[110],"evaluation":[111],"shows":[112],"centroids,":[116],"their":[119],"outputs,":[123],"as":[124,126],"well":[125],"aligned":[127],"reconstructions":[128,133],"the":[130,135],"exact":[131],"view":[132],"input":[136],"with":[138],"high":[139],"quality.":[140]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}